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- PDB-2ljz: Structure of the C-terminal domain of HPV16 E6 oncoprotein -

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Basic information

Entry
Database: PDB / ID: 2ljz
TitleStructure of the C-terminal domain of HPV16 E6 oncoprotein
ComponentsProtein E6
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / PDZ domain binding / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
E6 early regulatory protein / CRO Repressor / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman papillomavirus
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZanier, K. / Muhamed Sidi, A. / Boulade-Ladame, C. / Rybin, V. / Chappelle, A. / Atkinson, A. / Kieffer, B. / Trave, G.
CitationJournal: Structure / Year: 2012
Title: Solution Structure Analysis of the HPV16 E6 Oncoprotein Reveals a Self-Association Mechanism Required for E6-Mediated Degradation of p53.
Authors: Zanier, K. / Ould M'hamed Ould Sidi, A. / Boulade-Ladame, C. / Rybin, V. / Chappelle, A. / Atkinson, A. / Kieffer, B. / Trave, G.
History
DepositionSep 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9712
Polymers8,9051
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein E6


Mass: 8905.230 Da / Num. of mol.: 1 / Fragment: Zinc finger containing residues 87-158 / Mutation: C80S, C97S, C111S, C140S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus / Gene: E6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03126
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of the C-terminal zinc-binding domain of HPV16 E6
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1423D HNCA
1523D HN(CA)CB
1623D HN(CO)CA
1723D HBHA(CO)NH
1823D (H)CCH-TOCSY
1923D (H)CCH-COSY
11023D 1H-15N NOESY
11123D 1H-13C NOESY aliphatic
11212D 1H-1H NOESY
11312D 1H-1H NOESY
NMR detailsText: The structure was determined using noe and dihedral angle restraints

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM E6, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] E6, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 15N] E6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mME6-11
1 mME6-2[U-100% 13C; U-100% 15N]2
1 mME6-3[U-100% 15N]3
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 286 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE9502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.8.3Keller and Wuthrichdata analysis
ATNOS/CANDIDHerrmann, Guntert and Wuthrichpeak picking
ATNOS/CANDIDHerrmann, Guntert and Wuthrichautomatic noe assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1464 / NOE intraresidue total count: 370 / NOE long range total count: 371 / NOE medium range total count: 357 / NOE sequential total count: 366 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 56 / Protein psi angle constraints total count: 56
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.15 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 3.54 ° / Maximum upper distance constraint violation: 0.47 Å
NMR ensemble rmsDistance rms dev: 0.043 Å / Distance rms dev error: 0.001 Å

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